The iPad doesn't have folders per se (it does, but they are never exposed to the user).
Safari is the web browser, and HTML5 is basically a "web page". It's not a video format. HTML5 has a video tag, but the video is not HMTL5 video, it's whatever format the video is in.
You cannot put HTML5 onto the iPad directly. You can view it using the built-in web browser (Safari) which is going to have to download it from a network. As it turns out, Apple has provided a mechanism to create file on a website that lists all of the files the site uses, and with that, copy the files to your iOS device and make an icon on your home screen. To do that, you'll need to create the file and alter the starting page. See here for some documentation: https://developer.apple.com/library/safari/#documentation/iPhone/Conceptual/Safa riJSDatabaseGuide/OfflineApplicationCache/OfflineApplicationCache.html
Once you've added the approrpriate headers and created the necessary manifest file, you can then browse your HTML5 (yes, you will need a web server running on your computer - this won't work using the sync cable) page using the browser, and click the "Send" button in the browser (box with an arrow arcing out of it) and select "Add to Home Screen". Note that are limits on how much data can be stored in the offline cache.
That said, a couple of things: its not illegal distribution of your material if you authorize it. If you put your file on a service (a web host) to retrieve it later, then it's not illegal distribution. Moreover, you could password protect the directory where you store it such that only authorized persons could see it.
If you still prefer not to do that, however, by far the EASIEST thing to do is skip HTML5 altogether. If you aren't going to publicly share the presentation to a wider audience through their browsers, then it's an unnecessary step. The iOS app Documents2Go allows you to put your Powerpoint presentations directly in the Documents2Go data folder and present them - without translation. Keep in mind that not 100% of the features of Powerpoint are supported, but more so than your HTML5 translation.
If you are using a Mac, then Apple's Keynote application (for iOS and OS X) is an even a better choice. They sync through Apple's iCloud service and work really well - even allowing for previews and presenter notes (something you wouldn't have if mirroring your web browser).